Started by upstream project "BIOFORMATS-test-repo" build number 78
originally caused by:
Started by upstream project "Trigger" build number 86
originally caused by:
Started by timer
Running as SYSTEM
Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@3
[BIOFORMATS-test-folder@3] $ /bin/bash -xe /tmp/jenkins1698105983368942636.sh
+ '[' mrc = slidebook ']'
++ date +%u
+ '[' 3 -le 1 ']'
+ sudo docker run --rm --name BIOFORMATS-test-folder_11841_merge_ci -v /uod/idr/repos/curated/mrc:/data -v /uod/idr-scratch/merge-ci/curated/mrc:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12
Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml
[echo] isSnapshot = true
init-title:
[echo] ----------=========== bio-formats-testing-framework ===========----------
init-timestamp:
init:
copy-resources:
compile:
[resolver:resolve] Resolving artifacts
compile-tests:
[resolver:resolve] Resolving artifacts
[javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test
[javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[javac] 1 warning
test-automated:
[testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket
[testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket
[testng] File leak detector installed
[testng] 01:36:49,315 |-INFO in ch.qos.logback.classic.LoggerContext[default] - This is logback-classic version 1.3.14
[testng] 01:36:49,316 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - No custom configurators were discovered as a service.
[testng] 01:36:49,316 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:36:49,317 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.joran.SerializedModelConfigurator
[testng] 01:36:49,318 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.scmo]
[testng] 01:36:49,318 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.scmo]
[testng] 01:36:49,318 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.joran.SerializedModelConfigurator.configure() call lasted 1 milliseconds. ExecutionStatus=INVOKE_NEXT_IF_ANY
[testng] 01:36:49,318 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Trying to configure with ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:36:49,319 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - Constructed configurator of type class ch.qos.logback.classic.util.DefaultJoranConfigurator
[testng] 01:36:49,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [${logback.configurationFile}]
[testng] 01:36:49,319 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
[testng] 01:36:49,320 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [file:/bio-formats-build/bioformats/components/test-suite/logback.xml]
[testng] 01:36:49,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout]
[testng] 01:36:49,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
[testng] 01:36:49,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT]
[testng] 01:36:49,509 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender]
[testng] 01:36:49,515 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG
[testng] 01:36:49,515 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO
[testng] 01:36:49,515 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT]
[testng] 01:36:49,515 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng]
[testng] 01:36:49,515 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@576d5deb - End of configuration.
[testng] 01:36:49,516 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@6fdbe764 - Registering current configuration as safe fallback point
[testng] 01:36:49,516 |-INFO in ch.qos.logback.classic.util.ContextInitializer@d6e7bab - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 197 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY
[testng] [2024-05-29 01:36:49,525] [main] java.version = 17.0.2
[testng] 01:36:49,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main]
[testng] 01:36:49,528 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:49,569 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-05-29_01-36-49.log]
[testng] 01:36:49,571 |-INFO in ch.qos.logback.core.sift.SiftProcessor@37313c65 - End of configuration.
[testng] [2024-05-29 01:36:49,573] [main] testng.directory = /data
[testng] [2024-05-29 01:36:49,573] [main] testng.configDirectory = /config
[testng] [2024-05-29 01:36:49,582] [main] testng.multiplier = 1.0
[testng] [2024-05-29 01:36:49,583] [main] testng.in-memory = false
[testng] [2024-05-29 01:36:49,583] [main] testng.allow-missing = false
[testng] [2024-05-29 01:36:49,583] [main] user.language = en
[testng] [2024-05-29 01:36:49,583] [main] user.country = ${user.country}
[testng] [2024-05-29 01:36:49,583] [main] Maximum heap size = 15360 MB
[testng] Scanning for files...
[testng] [2024-05-29 01:36:50,761] [main] ----------------------------------------
[testng] [2024-05-29 01:36:50,761] [main] Total files: 20
[testng] [2024-05-29 01:36:50,761] [main] Scan time: 1.178 s (58 ms/file)
[testng] [2024-05-29 01:36:50,761] [main] ----------------------------------------
[testng] Building list of tests...
[testng] Ready to test 20 files
[testng] [TestNG] Running:
[testng] Bio-Formats software test suite
[testng]
[testng] [2024-05-29 01:36:51,215] [pool-1-thread-1] Initializing /data/ticket-10073/wtjoin4.rec:
[testng] 01:36:51,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1]
[testng] 01:36:51,215 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,216 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-05-29_01-36-51.log]
[testng] 01:36:51,217 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4f606a00 - End of configuration.
[testng] [2024-05-29 01:36:51,249] [pool-1-thread-12] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map:
[testng] 01:36:51,250 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12]
[testng] 01:36:51,251 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,254 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-05-29_01-36-51.log]
[testng] 01:36:51,254 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1f564c66 - End of configuration.
[testng] [2024-05-29 01:36:51,281] [pool-1-thread-11] Initializing /data/dan/three.mrc:
[testng] 01:36:51,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11]
[testng] 01:36:51,282 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,282 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-05-29_01-36-51.log]
[testng] 01:36:51,283 |-INFO in ch.qos.logback.core.sift.SiftProcessor@27442a3b - End of configuration.
[testng] [2024-05-29 01:36:51,299] [pool-1-thread-10] Initializing /data/ascb/cfa1071.mrc:
[testng] 01:36:51,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10]
[testng] 01:36:51,299 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,300 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-05-29_01-36-51.log]
[testng] 01:36:51,300 |-INFO in ch.qos.logback.core.sift.SiftProcessor@71559fa0 - End of configuration.
[testng] [2024-05-29 01:36:51,314] [pool-1-thread-9] Initializing /data/bioformats2raw-198/test_uint8.mrc:
[testng] 01:36:51,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9]
[testng] 01:36:51,314 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,315 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-05-29_01-36-51.log]
[testng] 01:36:51,315 |-INFO in ch.qos.logback.core.sift.SiftProcessor@4e49da5f - End of configuration.
[testng] [2024-05-29 01:36:51,324] [pool-1-thread-8] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc:
[testng] 01:36:51,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8]
[testng] 01:36:51,324 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,325 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-05-29_01-36-51.log]
[testng] 01:36:51,325 |-INFO in ch.qos.logback.core.sift.SiftProcessor@516639ac - End of configuration.
[testng] [2024-05-29 01:36:51,345] [pool-1-thread-7] Initializing /data/strand/Series1_A.mrc:
[testng] 01:36:51,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7]
[testng] 01:36:51,345 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,358 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-05-29_01-36-51.log]
[testng] 01:36:51,358 |-INFO in ch.qos.logback.core.sift.SiftProcessor@66ffc635 - End of configuration.
[testng] [2024-05-29 01:36:51,398] [pool-1-thread-6] Initializing /data/jcb/thylakoid5.rec:
[testng] 01:36:51,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6]
[testng] 01:36:51,399 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,400 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-05-29_01-36-51.log]
[testng] 01:36:51,400 |-INFO in ch.qos.logback.core.sift.SiftProcessor@43043779 - End of configuration.
[testng] [2024-05-29 01:36:51,420] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc:
[testng] 01:36:51,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5]
[testng] 01:36:51,431 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,432 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-05-29_01-36-51.log]
[testng] 01:36:51,433 |-INFO in ch.qos.logback.core.sift.SiftProcessor@417ee16a - End of configuration.
[testng] [2024-05-29 01:36:51,468] [pool-1-thread-4] Initializing /data/ascb/c191.st:
[testng] 01:36:51,468 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4]
[testng] 01:36:51,469 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,470 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-05-29_01-36-51.log]
[testng] 01:36:51,470 |-INFO in ch.qos.logback.core.sift.SiftProcessor@60dfd808 - End of configuration.
[testng] [2024-05-29 01:36:51,486] [pool-1-thread-3] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc:
[testng] 01:36:51,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3]
[testng] 01:36:51,486 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,487 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-05-29_01-36-51.log]
[testng] 01:36:51,487 |-INFO in ch.qos.logback.core.sift.SiftProcessor@25cfda94 - End of configuration.
[testng] [2024-05-29 01:36:51,500] [pool-1-thread-2] Initializing /data/samples/golgi.mrc:
[testng] 01:36:51,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2]
[testng] 01:36:51,500 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender]
[testng] 01:36:51,501 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-05-29_01-36-51.log]
[testng] 01:36:51,501 |-INFO in ch.qos.logback.core.sift.SiftProcessor@182319d1 - End of configuration.
[testng] [2024-05-29 01:36:52,519] [pool-1-thread-12] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc:
[testng] [2024-05-29 01:36:52,535] [pool-1-thread-9] Initializing /data/dan/one.mrc:
[testng] [2024-05-29 01:36:52,759] [pool-1-thread-2] Initializing /data/samples/1160.mrc:
[testng] [2024-05-29 01:36:52,773] [pool-1-thread-8] Initializing /data/dan/two.mrc:
[testng] [2024-05-29 01:36:52,784] [pool-1-thread-3] Initializing /data/ascb/514_9903.mrc:
[testng] [2024-05-29 01:36:52,794] [pool-1-thread-5] Initializing /data/ascb/c191ali.mrc:
[testng] [2024-05-29 01:36:52,854] [pool-1-thread-4] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc:
[testng] [2024-05-29 01:36:52,993] [pool-1-thread-6] Initializing /data/jcb/thyl-apr23-4.rec:
[testng]
[testng] ===============================================
[testng] Bio-Formats software test suite
[testng] Total tests run: 1060, Failures: 0, Skips: 0
[testng] ===============================================
[testng]
BUILD SUCCESSFUL
Total time: 12 seconds
Finished: SUCCESS